Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders

Mutation spectrum of thalassemia among pre-pregnant adults in the Jiangsu Province by capillary electrophoresis-based multiplex PCR assay

BACKGROUND

Thalassemia is a common genetic disorder in southwestern China, and an increasing number of cases from eastern China have been recently reported. Here, we developed a rapid, convenient, and accurate assay to evaluate the mutation spectrum of thalassemia in eastern China.

METHODS

A carrier screening assay for 61 hotspot variants among HBA1/HBA2 and HBB (OMIM: 141800, 141850, and 141900) genes was developed by SNaPshot/high-throughput ligation-dependent probe amplification (HLPA) technology. We used this assay to detect the mutation spectrum of thalassemia in individuals from eastern China and compared with the data collected from literatures focused on southern and northern China for variant distribution.

RESULTS

Among 4276 tested individuals, 2.62% (112/4276) were α-thalassemia carriers, with 90 carrying one deletion or mutation and 22 carrying two deletions. 0.40% (17/4276) were β-thalassemia carriers, and the most common variant of β-thalassemia was c.126_129delCTTT (29.41%) followed by c.316-197C>T (23.53%). The genotype distribution in our study was similar to those from southern China populations.

CONCLUSION

The Chinese population from different regions presented comparable mutation spectrum of thalassemia, and the SNaPshot/HLPA technique may serve as a capable assay for a routine genetic test in clinical practice with its accurate, rapid, and inexpensive advantage.

Use of expanded carrier screening for retrospective diagnosis of two deceased siblings with Van Maldergem syndrome 2: case report

Van Maldergem syndrome (VMLDS) is a recessive disease which affects multiple organs including the face, ear, and limb extremities. It can be caused by pathogenic variants in either the gene DCHS1 or FAT4. Diagnosis of VMLDS is complicated, especially regarding its similarity of symptoms to Hennekam syndrome, another disorder caused by FAT4 variants. Reported patients are two infantile siblings with multiple congenital anomalies, who deceased without clinical diagnosis. Whole exome sequencing was exploited for expanded carrier screening (ECS) of their parents, which revealed a novel splicing variant in the gene FAT4, NM_024582.6: c.7018+1G>A. In silico analysis of the variant indicates loss of canonical donor splice site of intron 6. This variant is classified as pathogenic based on ACMG criteria. Reverse phenotyping of patients resulted in likely diagnosis of VMLDS2. This study reaffirms the possibility of using ECS, leading to the genetic diagnosis of a rare disease with complicated clinical features.

A capillary electrophoresis-based multiplex PCR assay for expanded carrier screening in the eastern Han Chinese population

Expanded carrier screening, a type of reproductive genetic testing for couples, has gained tremendous popularity for assessing the risk of passing on certain genetic conditions to offspring. Here, a carrier screening assay for 448 pathogenic variants was developed using capillary electrophoresis-based multiplex PCR technology. The capillary electrophoresis-based multiplex PCR assay achieved a sensitivity, specificity, and accuracy of 97.4%, 100%, and 99.6%, respectively, in detecting the specific variants. Among the 1915 couples (3830 individuals), 708 individuals (18.5%) were identified as carriers for at least one condition. Of the 708 carriers, 633 (89.4%) were heterozygous for one condition, 71 (10.0%) for two disorders, 3 (0.4%) for three disorders, and 1 (0.1%) for four disorders. Meanwhile, 30 (1.57%) couples were identified as at‐risk couples. This study describes an inexpensive and effective method for expanded carrier screening. The simplicity and accuracy of this approach will facilitate the clinical implementation of expanded carrier screening.

A patient with compound heterozygosity of SMPD4: Another example of utility of exome-based copy number analysis in autosomal recessive disorders

For the efficient diagnosis of rare and undiagnosed diseases, the parallel detection of copy number variants (CNVs) and single nucleotide variants using exome analysis is required. Recently, our group reported the usefulness of a program called EXCAVATOR2, which screens for CNVs from aligned exome data in bam format. This method is expected to contribute to the identification of structural variants and to improve the diagnosis rate, especially for the diagnosis of autosomal recessive disease, when a conventional exome analysis identifies a pathogenic variant in one allele but not the other. Here we report a 2-year-old Japanese boy with an undiagnosed disease. He had severe neonatal asphyxia, severe intellectual disability, intractable seizures, cerebellar and brainstem hypoplasia and dysmorphic features including a prominent supraorbital ridge, thin upper lip, and prominent antihelix. An exome analysis reinforced with a copy number analysis using the EXCAVATOR2 method revealed that the patient had a hemizygous variant in chr2(GRCh37):g.130925108G>A, NM_017951.4 c.832C>T, p.(Arg278*) in SMPD4 that was derived from his father and a deletion of SMPD4 derived from his mother. The presence of the deletion spanning SMPD4 was confirmed by short-read and long-read whole-genome sequencing. The successful diagnosis of this reported patient demonstrates the diagnostic utility of EXCAVATOR2 and overcomes the weakness of exome analysis for the detection of autosomal recessive diseases in nonconsanguineous families, significantly impacting genetic counseling for family planning.

Whole Exome Sequencing Is the Minimal Technological Approach in Probands Born to Consanguineous Couples

We report on two siblings suffering from different pathogenic conditions, born to consanguineous parents. A multigene panel for brain malformations and microcephaly identified the homozygous splicing variant NM_005886.3:c.1416+1del in the KATNB1 gene in the older sister. On the other hand, exome sequencing revealed the homozygous frameshift variant NM_005245.4:c.9729del in the FAT1 gene in the younger sister, who had a more complex phenotype: in addition to bilateral anophthalmia and heart defects, she showed a right split foot with 4 toes, 5 metacarpals, second toe duplication and preaxial polydactyly on the right hand. These features have been never reported before in patients with pathogenic FAT1 variants and support the role of this gene in the development of limb buds. Notably, each parent was heterozygous for both of these variants, which were ultra-rare and rare, respectively. This study raises awareness about the value of using whole exome/genome sequencing rather than targeted gene panels when testing affected offspring born to consanguineous couples. In this way, exomic data from the parents are also made available for carrier screening, to identify heterozygous pathogenetic and likely pathogenetic variants in genes responsible for other recessive conditions, which may pose a risk for subsequent pregnancies.

Präimplantationsdiagnostik für monogene Erkrankungen am PID-Zentrum Regensburg

Wir berichten über die Erfahrungen unseres PID-Zentrums bei der Präimplantationsdiagnostik (PID) für 149 Familien mit hohem Risiko für eine monogene Erkrankung bei den Nachkommen und die Ergebnisse aus 316 PID-Zyklen. Seit 2001 wurden bei uns insgesamt 251 Diagnostikzyklen mittels Polkörperdiagnostik (PKD) durchgeführt. Nach der Zulassung unserer Gruppe als PID-Zentrum im Juni 2015 haben wir inzwischen für 45 Familien insgesamt 65 Trophektoderm-Diagnostikzyklen (TED) nach Trophektoderm (TE)-Biopsie durchgeführt (1,4/Familie). Unsere vorläufigen Daten bestätigen eine hohe Diagnoseeffizienz beider Verfahren mit Verdopplung der klinischen Schwangerschaftsrate pro Transfer nach TED auf 48,2 % verglichen mit 22,9 % nach PKD. Bei einer durchschnittlichen Rate von 4,3 verfügbaren Blastozysten pro TED-Zyklus ist die Rate von Zyklen ohne transferierbare Embryonen mit 27,7 % (für 6/45 Familien = 13,3 %) erwartungsgemäß höher als bei der PKD (14,7 %) für durchschnittlich 8 Eizellen pro Zyklus mit erfolgreicher Biopsie beider Polkörper. Schon mit dem ersten Transfer konnte jedoch nach TED für 55,3 % der Paare eine klinische Schwangerschaft erreicht werden. Insgesamt ermöglichte die TED kumulativ nach durchschnittlich 1,4 Transferen eine klinische Schwangerschaft für 68,5 % der Familien mit Transfer und insgesamt eine schonendere Behandlung mit weniger TED-Zyklen (PKD: kumulativ 40,3 % nach 2,3 Transferen), weniger Hormonstimulationen und entsprechend auch geringeren Kosten. Insbesondere die Subgruppe der weiblichen Überträgerinnen von Repeaterkrankungen mit insgesamt niedrigeren Erfolgschancen scheint nach unseren vorläufigen Daten von der TED zu profitieren.

Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?

Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of NGS-based genetic testing in the context of rare disease diagnosis. We highlight the role of artificial intelligence (AI) in enhancing understanding and prioritization of variance in the clinical setting and propose deep learning frameworks for further investigation.

Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project

Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.